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Yorodumi- PDB-2pn2: CRYSTAL STRUCTURE OF A PUTATIVE OSMOTIC STRESS INDUCED AND DETOXI... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pn2 | ||||||
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Title | CRYSTAL STRUCTURE OF A PUTATIVE OSMOTIC STRESS INDUCED AND DETOXIFICATION RESPONSE PROTEIN (PSYC_0566) FROM PSYCHROBACTER ARCTICUS 273-4 AT 2.15 A RESOLUTION | ||||||
Components | Uncharacterized protein | ||||||
Keywords | SIGNALING PROTEIN / PUTATIVE OSMOTIC STRESS INDUCED AND DETOXIFICATION RESPONSE PROTEIN / STRUCTURAL GENOMICS / JOINT CENTER FOR STRUCTURAL GENOMICS / JCSG / PROTEIN STRUCTURE INITIATIVE / PSI-2 | ||||||
Function / homology | OsmC/Ohr family / OsmC/Ohr superfamily / OsmC-like protein / K homology (KH) domain / GMP Synthetase; Chain A, domain 3 / K homology domain-like, alpha/beta / 2-Layer Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Psychrobacter arcticus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of uncharacterized protein (YP_263861.1) from Psychrobacter arcticus 273-4 at 2.15 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAINS. SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. | ||||||
Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pn2.cif.gz | 40.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pn2.ent.gz | 29.6 KB | Display | PDB format |
PDBx/mmJSON format | 2pn2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2pn2_validation.pdf.gz | 435.5 KB | Display | wwPDB validaton report |
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Full document | 2pn2_full_validation.pdf.gz | 436.9 KB | Display | |
Data in XML | 2pn2_validation.xml.gz | 8 KB | Display | |
Data in CIF | 2pn2_validation.cif.gz | 10.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pn/2pn2 ftp://data.pdbj.org/pub/pdb/validation_reports/pn/2pn2 | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
#1: Protein | Mass: 17462.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Psychrobacter arcticus (bacteria) / Strain: 273-4 / Gene: YP_263861.1, Psyc_0566 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q4FU81 | ||||
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#2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.01 Å3/Da / Density % sol: 38.69 % Description: ICE RINGS WERE EXCLUDED DURING DATA INTEGRATION BY MOSFLM |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.43 Details: NANODROP, 0.2M Ammonium sulfate, 30.5% PEG MME 2000, 0.1M Sodium acetate pH 4.43, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91162, 0.97939, 0.97922 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 1, 2007 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.95→36.466 Å / Num. obs: 8085 / % possible obs: 76.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 11.4 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.95→36.466 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.931 / SU B: 7.676 / SU ML: 0.111 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.252 / ESU R Free: 0.201 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. CL AND SO4 IONS FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 4. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 5. RESIDUES 132-136 ARE DISORDERED AND ARE NOT MODELED. 6. THE RESOLUTION SHELLS CORRESPONDING TO ICE RINGS WERE REMOVED DURING THE INTEGRATION OF THE DATA. THIS RESULTED IN LOWER COMPLETENESS. 7. THE NOMINAL RESOLUTION IS 2.15 A WITH 1570 OBSERVED REFLECTIONS BETWEEN 2.15-1.95 (59.8% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.711 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→36.466 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2.001 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 5.368 Å / Origin y: -1.96 Å / Origin z: 23.018 Å
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Refinement TLS group | Selection: ALL |